I finally got around to following the sage advice of putting witness marks on the Y stepper gears and noticed that mine don’t look like the usual pictures I have seen. The shaft is recessed into the center of the gear such that you can’t really mark it easily.
I have the Pro XXL. Is this normal? Are mine misaligned? I don’t have much room left on the side rails to shift that belt.
There is nothing wrong. The stepper motors only have a fixed length shaft. The SO4 machines increased the belt width but use the same stepper motors they use. So just reach in with a fine line sharpie and mark your shaft.